1 /**
2  * UGENE - Integrated Bioinformatics Tools.
3  * Copyright (C) 2008-2021 UniPro <ugene@unipro.ru>
4  * http://ugene.net
5  *
6  * This program is free software; you can redistribute it and/or
7  * modify it under the terms of the GNU General Public License
8  * as published by the Free Software Foundation; either version 2
9  * of the License, or (at your option) any later version.
10  *
11  * This program is distributed in the hope that it will be useful,
12  * but WITHOUT ANY WARRANTY; without even the implied warranty of
13  * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
14  * GNU General Public License for more details.
15  *
16  * You should have received a copy of the GNU General Public License
17  * along with this program; if not, write to the Free Software
18  * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston,
19  * MA 02110-1301, USA.
20  */
21 
22 #ifndef _U2_HMMSEARCH_TASK_H_
23 #define _U2_HMMSEARCH_TASK_H_
24 
25 #include <QMutex>
26 
27 #include <U2Core/AnnotationData.h>
28 #include <U2Core/DNASequence.h>
29 #include <U2Core/SequenceWalkerTask.h>
30 #include <U2Core/Task.h>
31 #include <U2Core/U2Region.h>
32 
33 #include "HMMIO.h"
34 #include "uhmmsearch.h"
35 
36 struct plan7_s;
37 
38 namespace U2 {
39 
40 class DNATranslation;
41 
42 class HMMSearchTaskResult {
43 public:
HMMSearchTaskResult()44     HMMSearchTaskResult()
45         : evalue(0), score(0), onCompl(false), onAmino(false), borderResult(false), filtered(false) {
46     }
47     float evalue;
48     float score;
49     bool onCompl;
50     bool onAmino;
51     bool borderResult;
52     bool filtered;
53     U2Region r;
54 };
55 
56 class HMMSearchTask : public Task, SequenceWalkerCallback {
57     Q_OBJECT
58 public:
59     HMMSearchTask(plan7_s *hmm, const DNASequence &seq, const UHMMSearchSettings &s);
60 
61     HMMSearchTask(const QString &hFile, const DNASequence &seq, const UHMMSearchSettings &s);
62 
63     virtual void prepare();
64 
getResults()65     const QList<HMMSearchTaskResult> &getResults() const {
66         return results;
67     }
68 
69     virtual void onRegion(SequenceWalkerSubtask *t, TaskStateInfo &stateInfo);
70 
71     Task::ReportResult report();
72 
73     QList<SharedAnnotationData> getResultsAsAnnotations(U2FeatureType type, const QString &name) const;
74 
75     QList<Task *> onSubTaskFinished(Task *subTask);
76 
77 private:
78     bool checkAlphabets(int hmmAl, const DNAAlphabet *seqAl, DNATranslation *&complTrans, DNATranslation *&aminoTrans);
79 
80     SequenceWalkerTask *getSWSubtask();
81 
82 private:
83     plan7_s *hmm;
84     DNASequence seq;
85     UHMMSearchSettings settings;
86     DNATranslation *complTrans;
87     DNATranslation *aminoTrans;
88     QList<HMMSearchTaskResult> results;
89     QList<HMMSearchTaskResult> overlaps;
90     QString fName;
91     QMutex lock;
92     HMMReadTask *readHMMTask;
93     SequenceWalkerTask *swTask;
94 };
95 
96 }  // namespace U2
97 #endif
98